› 3bbd

X-ray diffraction
2.15Å resolution

M. jannaschii Nep1 complexed with S-adenosyl-homocysteine

Released:
DOI: 10.2210/pdb3bbd/pdb
PDB entry 3bbd coloured by chain, front view.
PDB entry 3bbd coloured by chain, side view.
PDB entry 3bbd coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
Taylor AB, Meyer B, Leal BZ, Kötter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wöhnert J
OpenAccess logo Nucleic Acids Res 36 1542-54 (2008)
PMID: 18208838

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176507 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal RNA small subunit methyltransferase Nep1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 205 amino acids
Theoretical weight: 24.45 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q57977 (Residues: 1-205; Coverage: 100%)
Gene names: MJ0557, nep1
Sequence domains: EMG1/NEP1 methyltransferase
Structure domains: Alpha/beta knot

Ligands and Environments

2 bound ligands:
Ligand SAH 2 x SAH
Ligand GOL 7 x GOL
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 84.894Å b: 91.121Å c: 93.713Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.221
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function.
Sloan et al. (2017)
2 more

2 mentions without citation

The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase.
Wurm et al. (2010)
1 more